rs9858542

A SNP in the BSN gene on chromosome 3. Its most notable genotype is A;A: 1.8x risk of Crohn's disease

Gene
BSN
Location
Chr 349,664,550 (GRCh38)
Highest magnitude
1.3Minor
Tested on
23andMe, AncestryDNA
Minor allele frequency
22%

Genotypes

As shown in 23andMe and AncestryDNA files.

  1. A;AMost notableBad1.8x risk of Crohn's diseaseMinor · 1.35% of people
  2. A;GBad1.1x risk Crohn's DiseaseMinor · 1.232% of people
  3. G;GNot ratednormalTypical · 0.064% of people

On SNPedia: (A;A), (A;G), (G;G). Magnitude rates how notable a genotype is from 0 to 10, not how risky it is.

Frequency

Share of each genotype in 11 HapMap populations.

  • AverageA;A 5% A;G 32% G;G 64%
  • European ancestry (Utah)A;A 4% A;G 43% G;G 53%
  • Han Chinese (Beijing)A;A 0% A;G 9% G;G 91%
  • Japanese (Tokyo)A;A 0% A;G 9% G;G 91%
  • Yoruba (Nigeria)A;A 8% A;G 29% G;G 63%
  • African ancestry (Southwest US)A;A 2% A;G 49% G;G 49%
  • Chinese (Denver)A;A 2% A;G 10% G;G 88%
  • Gujarati IndianA;A 5% A;G 36% G;G 59%
  • Luhya (Kenya)A;A 10% A;G 37% G;G 53%
  • Mexican ancestry (Los Angeles)A;A 3% A;G 40% G;G 57%
  • Maasai (Kenya)A;A 8% A;G 36% G;G 56%
  • TuscanA;A 8% A;G 52% G;G 40%

Conditions, medicines and genes

Notes

From SNPedia

Notes

rs9858542 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.09 (CI 0.96-1.24), and for homozygotes, 1.84 (CI 1.49-2.26).

Source and license

Adapted from rs9858542 on SNPedia, using a snapshot taken October 16, 2026. SNPedia content is shared under CC BY-NC-SA 3.0 US, and this page is shared under the same license.

SNPedia is a community-edited wiki. Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice. Magnitude is a community rating of how interesting a genotype is, not a risk score.